NiiVue-NiiMath

niivue is a neuroimaging visualization tool that can be embedded into web pages or standalone applications. niimath is a clone of fslmaths that provides many image processing commands. This web page shows how niimath (after being compiled to WebAssembly) can be used as a NiiVue plugin to allow rapid image processing using familiar commands.

Live Demo

Try out this repository in a live demo

Compiling

You can host your own instance locally, allowing you to tume this distribution.

git clone https://github.com/niivue/niivue-niimath
cd niivue-niimath
npm install
npm run dev

Commands

You can use many of the commands familiar to fslmaths users:

• bandpass : Butterworth filter, highpass and lowpass in Hz,TR in seconds (zero-phase 2*2nd order filtfilt)
• bptfm : Same as bptf but does not remove mean (emulates fslmaths < 5.0.7)
• bwlabel : Connected component labelling for non-zero voxels (conn sets neighbors: 6, 18, 26)
• c2h : reverse h2c transform
• ceil : round voxels upwards to the nearest integer
• crop : remove volumes, starts with 0 not 1! Inputting -1 for a size will set it to the full range
• dehaze : set dark voxels to zero (mode 1..5; higher yields more surviving voxels)
• detrend : remove linear trend (and mean) from input
• demean : remove average signal across volumes (requires 4D input)
• edt : estimate Euler Distance Transform (distance field). Assumes isotropic input
• floor : round voxels downwards to the nearest integer
• mod : modulus fractional remainder - same as '-rem' but includes fractions
• otsu : binarize image using Otsu''s method (mode 1..5; higher yields more bright voxels))
• power : raise the current image by following exponent
• h2c : convert CT scans from 'Hounsfield' to 'Cormack' units to emphasize soft tissue contrast
• resize : grow (>1) or shrink (<1) image. Method (0=nearest,1=linear,2=spline,3=Lanczos,4=Mitchell)\n");
• round : round voxels to the nearest integer
• sobel : fast edge detection
• sobel_binary : sobel creating binary edge
• tensor_2lower : convert FSL style upper triangle image to NIfTI standard lower triangle order
• tensor_2upper : convert NIfTI standard lower triangle image to FSL style upper triangle order
• tensor_decomp_lower : as tensor_decomp except input stores lower diagonal (AFNI, ANTS, Camino convention)
• trunc : truncates the decimal value from floating point value and returns integer value
• unsharp : edge enhancing unsharp mask (sigma in mm, not voxels; 1.0 is typical for amount (scl))
• dog : difference of gaussian with zero-crossing edges (positive and negative sigma mm)